As-far as drilling the floor of the slides goes, I do not see any real issue to restoring it to stock jetting and having-done the drilling, leaving it like that. The reason given is to allow the slides to move more-quickly, and since they are CV slides in the first place, and respond to a vacuum signal, a minor change in the orifice doesn't seem like such a significant change. I suppose if you wanted-to, you could epoxy them shut and re-drill to the stock dia. if you were going to remove the stage 7, like selling the bike & transferring the stage 7 kit to the next bike.
I have a stage 7 set of carbs not yet installed and am considering getting a spare VBoost manifold so I can have the butterfly replacement tubes instead so I can just swap both systems if I want to. I know you can just safety-wire the butterflies open if you don't want to remove them & replace them w/tubes. From reading here I also see some people leave the VBoost in-place even w/stage 7 installed.